Contacts of the helix formed by residues 112 - 124 (chain B) in PDB entry 6CKX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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765A GLU* 3.4 26.2 - - + +
101B PHE* 4.7 0.4 - - - -
111B LYS* 1.3 75.1 - - - +
113B CYS* 1.3 66.0 + - - +
114B LYS* 4.3 10.1 - - + +
115B ASP* 2.9 36.4 + - - +
116B ILE* 3.2 10.7 + - - +
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Residues in contact with CYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765A GLU* 3.1 18.1 + - - +
101B PHE* 3.8 19.7 - - + -
111B LYS 3.6 1.6 + - - -
112B LYS* 1.3 71.3 - - - +
114B LYS* 1.3 64.1 + - - +
116B ILE* 3.1 8.3 + - - +
117B ILE* 3.0 34.4 + - - +
137B LYS* 4.0 33.7 - - - -
140B VAL* 3.9 30.5 - - - -
141B MET* 4.1 9.4 - - - -
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765A GLU* 5.1 1.0 + - - +
112B LYS* 3.3 9.3 - - + +
113B CYS* 1.3 76.5 - - - +
115B ASP* 1.3 62.2 + - - +
117B ILE* 3.5 8.0 + - - +
118B LYS* 3.1 26.9 + - - +
137B LYS* 5.0 10.4 - - + +
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 3.8 16.9 - - + +
111B LYS* 5.2 7.6 - - + +
112B LYS* 2.9 38.5 + - - +
114B LYS* 1.3 74.0 - - - +
116B ILE* 1.3 63.6 + - - +
118B LYS* 4.0 6.7 - - - +
119B THR* 2.8 30.5 + - - -
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B VAL* 4.4 10.2 - - + +
64B LEU* 3.8 23.1 - - + -
66B LEU* 5.9 0.4 - - + -
97B ALA* 3.9 33.4 - - + +
100B LEU* 4.4 11.2 - - + +
101B PHE* 3.5 47.6 - - + +
111B LYS* 4.4 15.3 - - + -
112B LYS 3.2 6.5 + - - +
113B CYS* 3.1 11.9 + - - +
115B ASP* 1.3 74.0 - - - +
117B ILE* 1.3 64.8 + - + +
119B THR* 3.5 2.4 + - - -
120B ALA* 2.8 27.8 + - + +
140B VAL* 6.2 0.7 - - + -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B CYS* 3.0 24.3 + - - +
114B LYS* 3.7 9.0 - - - +
116B ILE* 1.3 78.4 - - + +
118B LYS* 1.3 67.7 + - - +
120B ALA* 3.0 6.0 + - - +
121B ARG* 2.8 23.0 + - + +
129B PHE* 3.9 15.3 - - + -
132B PHE* 4.2 13.5 - - + -
136B PRO* 3.7 43.1 - - + +
137B LYS* 4.4 9.2 - - + +
140B VAL* 4.1 18.4 - - + -
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LYS 3.1 17.2 + - - +
115B ASP* 4.0 8.3 - - - +
116B ILE 3.5 0.4 - - - -
117B ILE* 1.3 73.9 - - - +
119B THR* 1.3 58.3 + - - +
121B ARG* 3.2 7.5 + - - +
122B SER* 2.8 29.3 + - - -
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B VAL* 3.6 39.0 - - + +
63B ARG* 3.7 29.4 - - + +
64B LEU* 3.2 16.6 - - + +
115B ASP 2.8 18.4 + - - -
116B ILE 3.8 3.4 - - - -
118B LYS* 1.3 73.3 - - - +
120B ALA* 1.3 66.0 + - - +
122B SER* 2.6 24.0 + - - -
123B LEU* 3.2 10.0 + - + +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 3.7 28.7 - - + -
60B VAL* 4.1 6.7 - - + +
97B ALA* 5.2 3.4 - - + -
116B ILE 2.8 21.9 + - - +
117B ILE* 3.0 7.8 + - - +
119B THR* 1.3 73.1 - - - +
121B ARG* 1.3 63.2 + - - +
123B LEU* 3.0 4.5 + - - +
124B LEU* 3.0 30.9 + - + +
129B PHE* 4.6 2.5 - - + -
132B PHE* 4.3 17.0 - - + -
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ILE* 2.8 16.6 + - + +
118B LYS* 3.4 11.2 - - - +
120B ALA* 1.3 72.4 - - - +
122B SER* 1.3 62.7 + - - +
123B LEU 3.3 0.9 + - - -
124B LEU 3.1 25.9 + - - +
125B ASN* 3.8 0.8 - - - +
126B ASP* 2.8 41.8 + - - +
129B PHE* 3.6 51.7 - - + +
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ARG* 3.4 29.8 + - - -
118B LYS 2.8 13.1 + - - -
119B THR* 2.6 22.8 + - - -
121B ARG* 1.3 78.8 - - - +
123B LEU* 1.3 58.7 + - - +
124B LEU 4.5 1.9 - - - +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 4.7 10.8 - - + +
59B ASP* 3.7 23.8 - - + +
60B VAL* 3.7 44.2 - - + +
63B ARG* 3.5 24.9 - - - +
119B THR* 3.2 12.5 + - + +
120B ALA 3.0 7.8 + - - +
122B SER* 1.3 81.5 - - - +
124B LEU* 1.3 63.0 + - - +
128B GLN* 4.6 2.3 - - - +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 3.6 30.5 - - + -
93B TYR* 4.0 20.0 - - + -
120B ALA 3.0 18.6 + - - +
121B ARG* 3.1 23.0 + - - +
122B SER 4.5 2.6 - - - +
123B LEU* 1.3 83.1 - - - +
125B ASN* 1.3 63.8 + - - +
128B GLN* 3.6 33.9 - - + +
129B PHE* 4.1 13.5 - - + +
132B PHE* 3.8 27.6 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il